Parallel nucleic acid helices with hoogsteen base pairing: Symmetry and structure

Molecular structures for parallel DNA and RNA double helices with Hoogsteen pairing are proposed for the first time. The DNA helices have sugars in the C2′-endo region and the phosphodiester conformations are (trans, gauche^?), and the RNA helices have sugars in the C3′-endo region and the phosphodiester conformations are (gauche^?, gauche^?). A pseudorotational symmetry relates the two parallel strands of DNA helices and a screw symmetry relates the two strands of RNA helices, which have an associated tilt of the The conformational space of parallel helices with Hoogsteen base pairing, unlike the Watson-Crick duplex, is highly restricted due to the unique positioning of the symmetry axis in the former case. The features of the parallel double helix with Hoogsteen pairing are compared with the Watson-Crick duplex and the corresponding triple helix. © 1994 John Wiley & Sons, Inc.     

PackHelix: a tool for helix-sheet packing during protein structure prediction

The three‐dimensional structure of a protein is organized around the packing of its secondary structure elements. Predicting the topology and constructing the geometry of structural motifs involving α‐helices and/or β‐strands are therefore key steps for accurate prediction of protein structure. While many efforts have focused on how to pack helices and on how to sample exhaustively the topologies and geometries of multiple strands forming a β‐sheet in a protein, there has been little progress on generating native‐like packings of helices on sheets. We describe a method that can generate the packing of multiple helices on a given β‐sheet for αβα sandwich type protein folds. This method mines the results of a statistical analysis of the conformations of αβ₂ motifs in protein structures to provide input values for the geometric attributes of the packing of a helix on a sheet. It then proceeds with a geometric builder that generates multiple arrangements of the helices on the sheet of interest by sampling through these values and performing consistency checks that guarantee proper loop geometry between the helices and the strands, minimal number of collisions between the helices, and proper formation of a hydrophobic core. The method is implemented as a module of ProteinShop. Our results show that it produces structures that are within 4–6 Å RMSD of the native one, regardless of the number of helices that need to be packed, though this number may increase if the protein has several helices between two consecutive strands in the sequence that pack on the sheet formed by these two strands. Proteins 2011; Published 2011 Wiley‐Liss, Inc.     

Double helix formation in α‐peptides: a theoretical study

A complete overview on all possible hydrogen bonding patterns of double helices with antiparallel and parallel strand orientation in α‐peptide sequences is provided on the basis of ab initio molecular orbital theory. The most stable representatives belong to the group of antiparallel helices. The study on side chain influence shows that these double helices can only be realized if the strands are composed of L ‐ and D ‐amino acids in alternate order. The stability of the double helices is compared with that of competing single‐stranded helices. The data contribute to an understanding of secondary structure formation in peptides and provide a basis for a rational design of membrane channels. Copyright © 2010 European Peptide Society and John Wiley & Sons, Ltd.     

Electron Microscopic Observations of the Structure of Sieve-connexions in the Phloem of Angiosperms and Gymnosperms

The sieve elements of Pinus silvestris L., Sorbus aucupariaL., Vitis vinifera L., and Cucurbita pepo L. have been examinedelectron microscopically in ultra-thin section, and the structuresof the corresponding sieve areas or sieve plates have been describedand compared. In Pinus the sieve areas contain groups of connectingstrands which enter the wall from the lumen side as individualsbut coalesce within it in the median cavity. This cavity hasdeveloped by wall breakdown in the middle lamella and primarywall region and corresponds to the median nodule visible undera light microscope. Neither in this nor in the other speciesobserved is there any visible closing membrane. Structural differences between the four species are shown tosuggest that the major evolutionary trend in the evolution ofspecialized conducting strands has been the enlargement of theconnecting strands from groups of small separate strands toa smaller number of larger strands as the median cavity becomesenlarged to form a canal through the wall. The connecting strands appear invariably to be dense, highlyosmiophilic and continuous with the cytoplasmic surface of thecell. No signs of micropores or of other tubular structure inthe strands have been found. The structures thus revealed aremore nearly compatible with active transport of materials acrossthe sieve plate than they are with any purely physical mechanism.It is suggested that they are incompatible with any mass flowhypothesis.     

Helix‐sheet packing in proteins

The three‐dimensional structure of a protein is organized around the packing of its secondary structure elements. Although much is known about the packing geometry observed between α‐helices and between β‐sheets, there has been little progress on characterizing helix–sheet interactions. We present an analysis of the conformation of αβ₂ motifs in proteins, corresponding to all occurrences of helices in contact with two strands that are hydrogen bonded. The geometry of the αβ₂ motif is characterized by the azimuthal angle θ between the helix axis and an average vector representing the two strands, the elevation angle ψ between the helix axis and the plane containing the two strands, and the distance D between the helix and the strands. We observe that the helix tends to align to the two strands, with a preference for an antiparallel orientation if the two strands are parallel; this preference is diminished for other topologies of the β‐sheet. Side‐chain packing at the interface between the helix and the strands is mostly hydrophobic, with a preference for aliphatic amino acids in the strand and aromatic amino acids in the helix. From the knowledge of the geometry and amino acid propensities of αβ₂ motifs in proteins, we have derived different statistical potentials that are shown to be efficient in picking native‐like conformations among a set of non‐native conformations in well‐known decoy datasets. The information on the geometry of αβ₂ motifs as well as the related statistical potentials have applications in the field of protein structure prediction. Proteins 2010. © 2010 Wiley‐Liss, Inc.     

Mechanisms of Reduction of the Stelar Pattern along Barley Roots

The stelar pattern along the seminal and nodal roots of barley (Hordeum vulgare L.) is gradually simplified due to a decreasing frequency of longitudinal cell division in the apical meristem. The decrease involves the proportion of stelar parenchyma, the number of vascular strands on the periphery of the stele and, in nodal roots with a more complex structure, the number of central metaxylem files. In spite of the fact that the stelar parenchyma is reduced in distal parts of the roots to approximately one half, the discontinuity of central and peripheral metaxylem is preserved. Reduction of the number of central metaxylem files is due to fusion. In the reduction of peripheral xylem and phloem strands, the development of certain xylem strands is discontinued and they are terminated blindly. Two phloem strands that had alternated radially with them, approach each other, coalesce and a single phloem strand continues to develop. In this way the regular alternation of phloem and xylem is re-established. The importance of fusions ensuring reduction of the functional continuity in vascular tissue by formation of a network structure must be stressed. This reduction mechanism is involved not only in files of the wide central metaxylem but also in phloem strands which are thus preferred over blindly terminating peripheral xylem strands.     

Geometrical principles of homomeric β‐barrels and β‐helices: Application to modeling amyloid protofilaments

Examples of homomeric β‐helices and β‐barrels have recently emerged. Here we generalize the theory for the shear number in β‐barrels to encompass β‐helices and homomeric structures. We introduce the concept of the “β‐strip,” the set of parallel or antiparallel neighboring strands, from which the whole helix can be generated giving it n‐fold rotational symmetry. In this context, the shear number is interpreted as the sum around the helix of the fixed register shift between neighboring identical β‐strips. Using this approach, we have derived relationships between helical width, pitch, angle between strand direction and helical axis, mass per length, register shift, and number of strands. The validity and unifying power of the method is demonstrated with known structures including α‐hemolysin, T4 phage spike, cylindrin, and the HET‐s(218‐289) prion. From reported dimensions measured by X‐ray fiber diffraction on amyloid fibrils, the relationships can be used to predict the register shift and the number of strands within amyloid protofilaments. This was used to construct models of transthyretin and Alzheimer β(40) amyloid protofilaments that comprise a single strip of in‐register β‐strands folded into a “β‐strip helix.” Results suggest both stabilization of an individual β‐strip helix and growth by addition of further β‐strip helices can involve the same pair of sequence segments associating with β‐sheet hydrogen bonding at the same register shift. This process would be aided by a repeat sequence. Hence, understanding how the register shift (as the distance between repeat sequences) relates to helical dimensions will be useful for nanotube design.     

Crystal structure of a putative oligopeptide-binding periplasmic protein from a hyperthermophile

Oligopeptide-binding proteins (Opps) are part of the ATP-binding cassette system, playing a crucial role in nutrient uptake and sensing the external environment in bacteria, including hyperthermophiles. Opps serve as a binding platform for diverse peptides; however, how these peptides are recognized by Opps is still largely unknown and few crystal structures of Opps from hyperthermophiles have been determined. To facilitate such an understanding, the crystal structure of a putative Opp, OppA from Thermotoga maritima (TmOppA), was solved at 2.6-Å resolution in the open conformation. TmOppA is composed of three domains. The N-terminal domain consists of twelve strands, nine helices, and four 3₁₀ helices, and the C-terminal domain consists of five strands, ten helices, and one 3₁₀ helix. These two domains are connected by the linker domain, which consists of two strands, three helices, and three 3₁₀ helices. Based on structural comparisons of TmOppA with other OppAs and binding studies, we suggest that TmOppA might be a periplasmic Opp. The most distinct feature of TmOppA is the insertion of two helices, which are lacking in other OppAs. A cavity volume between the N-terminal and C-terminal domains is suggested to be responsible for binding peptides of various lengths.     

Cooperative nonenzymic base recognition II. thermodynamics of the helix-coil transition of oligoadenylic + oligouridylic acids

The properties of oligonucleotide helices of adeuylic- and uridylic acid oligomers have been investigated by measurements of hypo-and hyperchromieity. High ionic strengths favor the formation of triple helices. Thus, the double helix-coil transition can be studied (without interference by triple helices) only at low ionic-strength. A “phase diagram” is given representing the T_m-values of the various transitions at different ionic strengths for the system A(pA)₁₇ + U(pU)₁₇. Oligonucleolides of chain lengths <8 always form both double and triple helices at the nucleotide concentrations required for base pairing. For this reason the double helix-coil transition without coupling of the triple helix equilibrium can only be measured for chain lengths higher than 7. Melting curves corresponding to this transition have been determined for chain lengths 8, 9, 10, 11, 14 and 18 at different concentrations. An increase in nucleotide concentration leads to an increase in melting temperature. The shorter the chain length the lower the T_m-value and the broader the helix-coil transition. The experimental transition curves have been analysed according to a staggering zipper model with consideration of the stacking of the adeuylic acid single strands and the electrostatic repulsion of tlip phosphate charges on opposite strands. The temperature dependence of the nucleation parameter has been accounted for by a slacking factor x. The stacking factor expresses the magnitude of the stacking enthalpy. By curve fitting xwas computed to be 0.7, corresponding to a stacking enthalpy of about S kcal/mole. The model described allows the reproduction of the experimental transition curves with relatively high accuracy. In an appendix the thermodynamic parameters of the stacking equilibrium of poly A and of the helix-coil equilibria of poly A + poly U at neutral pH are calculated (ΔH_A = ?7.9 kcal/mole for the poly A stacking and ΔH₁₂ = ?10.9 kcal/mole for the formation of the double helix from the randomly coiled single strands). A formula for the configurational entropy of polymers derived by Flory on the basis of a liquid lattice model is adapted to calculate the stacking entropies of adenylic oligomers.     

The physical organization of the cytoplasm in Myxococcus xanthus and the fine structure of its components

Summary The cytoplasmic components of Myxococcus xanthus were found to be helical strands of considerable length when examined in thin sections of cells. Similar structures were obtained in a population of isolated particles from fractionated cells. The width of the strands was estimated to be approximately 250 A, a single thread was about 50 A in width. It was suggested that the helices were fibrillar. The width of single fibrils was close to the resolving power of the instrument, about 10 A. No single ribosomes were found in thin sections of cells but most of the isolated particles were round, 100–250 A in diameter. The cytoplasmic strands were built of subunits of the size known for ribosomes which could be identified as such upon fragmentation of the strands. Crystal-like structures were found in this Gram-negative organism which, in some cases, comprised a large portion of the cell. The question was raised whether this type of fabric represents the true physical organization of the cytoplasm.Dedicated to Prof. Dr. W. Schwartz on his 70th birthday.     

中国梳蓟马属一新种（缨翅目：蓟马科）

记述中国梳蓟马属1新种:Ctenothrips dissimilis sp.nov.。该新种触角7节、腹部网状刻纹较浅,可明显区别于本属内其它种;雄虫和C.niger很相似,但C.niger腹部III-IV节腹板腺域为短圆形,该新种腺域为长椭圆形,同时触角节数和颜色也不同。模式标本保存于西北农林科技大学昆虫博物馆。     

A new armored searobin <Emphasis Type="Italic">Paraheminodus longirostralis</Emphasis> (Teleostei: Peristediidae) from New Caledonia

A new species of armored searobin, Paraheminodus longirostralis, is described from five specimens collected from New Caledonia at depths of 412–467 m. It is distinguishable from its three known congeners in having 34 bony plates in the upper lateral row, a forward-directed spine on each plate between the 23rd–26th and 31st–32nd plates in the upper lateral row, 6–7 + 1 + 20–21 = 27–28 gill rakers, an elongate body posterior to the anus (49.9–52.1% standard length), an elongate rostral projection (53.0–59.3% head length), short upper jaw (42.1–43.4% head length), an elongate pectoral fin (70.6–79.4% head length), and long preopercular spine (39.2–57.7% head length).     

Spermatogenesis in the inseminating African butterflyfish Pantodon buchholzi (Teleostei: Osteoglossiformes: Pantodontidae) with the revision of residual bodies formation

The aim of this study was to analyse spermatogenesis in the African butterflyfish, Pantodon buchholzi, using transmission electron microscopy and scanning electron microscopy. P. buchholzi is the most basal teleost that exhibits insemination and produces a highly complex introsperm with the most elongate midpiece known in teleost fishes. Their early stages (spermatogonia and spermatocytes) do not differ greatly from those of other fishes, with the exception of Golgi apparatus degradation appearing as spindle-shaped bodies (SSBs). In round, early spermatids, the development of the flagellum begins after the migration of the centriolar complex towards the nucleus. Later, the elongation of the midpiece coincides with the displacement of the mitochondria and their fusion to produce nine mitochondrial derivatives (MDs). In these spermatids, the nucleus is situated laterally to the midpiece, with condensing chromatin in the centre of the nucleus. Within the midpiece, the flagellum is located within a cytoplasmic canal and is surrounded by a cytoplasmic sleeve containing fibres, MDs and a great amount of cytoplasm located on one side. During the next phase, nuclear rotation, the highly condensed chromatin is displaced to a position above the centriolar apparatus, whereas chromatin-free nucleoplasm is transferred to the cytoplasm. Later, this nucleoplasm, still surrounded by the nuclear membrane, is eliminated into the cyst lumen as the nucleoplasmic packet. Within the highly elongate spermatids, other excess organelles (SSBs, endoplasmic reticulum and mitochondria) are eliminated as residual bodies (RBs). Fully developed spermatozoa, which contain conical-shaped nuclei, eventually coalesce to form unencapsulated sperm packets (spermatozeugmata) that are surrounded by RBs at the level of the extremely elongate midpieces. Later, RBs are removed at the periphery of the cyst by means of phagocytosis by Sertoli cells.     

蛋白质折叠速率与其氨基酸序列极性的关系

以大肠杆菌60个蛋白酶以及几种常见病毒（SARS病毒、艾滋病病毒、丙型肝炎病毒及乙型肝炎病毒）各蛋白质序列中的所有α-螺旋和β-折叠片段为研究对象,计算了各片段的折叠速率和平均极性,分别在各物种的α-螺旋和β-折叠两类二级结构片段中分析了二者的相关性。得到结论：不论是大肠杆菌中的蛋白酶还是病毒蛋白,其中的两类氨基酸片段的平均极性与折叠速率都是极显著相关的：对于所有的α片段,二者呈线性正相关,而对于所有的β片段,二者成线性负相关。结果证实了在蛋白质折叠中,氨基酸的极性起着重要的作用。     

Multi-strand β-sheet of Alzheimer Aβ(1–40) folds to β-strip helix: implication for protofilament formation

X-ray fiber diffraction experiments on Alzheimer Aβ(1–40) fibrils formed in an assembly process thought to simulate a portion of the pathophysiological process in Alzheimer's disease, indicated protofilaments with tilted β-strands rather than strands oriented perpendicular to the fibril axis as is usually interpreted from cross-β patterns. The protofilament width and tilt angle determined by these experiments were used to predict a β-strip helix model – a β-helix-like structure in which multiple identical polypeptide molecules assemble in-register to form a helical sheet structure such that the outer strands 1 and m join with a register shift t – with m = 11 and t = 22. Starting from untwisted β-sheets comprising 10, 11, and 12 strands, multiple explicit solvent molecular dynamics (MD) simulations were performed to determine whether the sheets form β-strip helices matching the dimensions of the experimentally measured protofilament. In the simulations, the predicted 11-strand sheets curled up to form a closed β-strip helix-like structure with dimensions matching experimental values, whereas the 10- and 12-strand sheets did not form a closed helical structure. The 12-strand structure did, however, show similarity to a cross-β structure determined by a solid-state NMR experiment. The 11-strand β-strip helix resembles a trans-membrane β-barrel which could explain the ability of small oligomers of Aβ(1–40) to form toxic ion channels. A further consequence of opposite sides of the 11-strand strip coming together at a register shift of 22 is end-to-end joins between neighboring β-strip helices, resulting in a protofilament that keeps growing in both directions.

Communicated by Ramaswamy H. Sarma     

A NEW SCIADOPITYACEOUS SEED CONE FROM THE UPPER CRETACEOUS OF HOKKAIDO,JAPAN

A sciadopityaceous seed cone, Sciadopityostrobus kerae, gen. et sp. nov., is described on the basis of a permineralized specimen from the Upper Cretaceous (Cenomanian–Coniacian) of Hokkaido, Japan. The peel method was applied for anatomical observations. The seed cone consists of a cone axis receiving numerous cone scale complexes that are arranged helically. Each complex generally has five inverted ovules that are oriented adaxially. The cone is similar to those of living Sciadopitys verticillata with respect to its peltate cone scale complex, with free apices of both bract and ovuliferous scale, trichomes on the bract, and a trifurcated ovuliferous scale strand. In the fossil, the bract and ovuliferous scale strands fuse with each other in the basal part of the cone scale complex, while S. verticillata bract and ovuliferous scale strands are derived separately from the vascular cylinder and remain separate throughout their length. The present specimen is one of the oldest records of structurally preserved cones that can be assigned to the family Sciadopityaceae.     

Cooperative effects in hydrogen-bonding of protein secondary structure elements: a systematic analysis of crystal data using Secbase

A systematic analysis of the hydrogen-bonding geometry in helices and beta sheets has been performed. The distances and angles between the backbone carbonyl O and amide N atoms were correlated considering more than 1500 protein chains in crystal structures determined to a resolution better than 1.5 A. They reveal statistically significant trends in the H-bond geometry across the different secondary structural elements. The analysis has been performed using Secbase, a modular extension of Relibase (Receptor Ligand Database) which integrates information about secondary structural elements assigned to individual protein structures with the various search facilities implemented into Relibase. A comparison of the mean hydrogen-bond distances in alpha helices and 3(10) helices of increasing length shows opposing trends. Whereas in alpha helices the mean H-bond distance shrinks with increasing helix length and turn number, the corresponding mean dimension in 3(10) helices expands in a comparable series. Comparing similarly the hydrogen-bond lengths in beta sheets there is no difference to be found between the mean H-bond length in antiparallel and parallel beta sheets along the strand direction. In contrast, an interesting systematic trend appears to be given for the hydrogen bonds perpendicular to the strands bridging across an extended sheet. With increasing number of accumulated strands, which results in a growing number of back-to-back piling hydrogen bonds across the strands, a slight decrease of the mean H-bond distance is apparent in parallel beta sheets whereas such trends are obviously not given in antiparallel beta sheets. This observation suggests that cooperative effects mutually polarizing spatially well-aligned hydrogen bonds are present either in alpha helices and parallel beta sheets whereas such influences seem to be lacking in 3(10) helices and antiparallel beta sheets.     

Native secondary structure topology has near minimum contact energy among all possible geometrically constrained topologies

Secondary structure topology in this article refers to the order and the direction of the secondary structures, such as helices and strands, with respect to the protein sequence. Even when the locations of the secondary structure Cα atoms are known, there are still (N!2^N)(M!2^M) different possible topologies for a protein with N helices and M strands. This work explored the question if the native topology is likely to be identified among a large set of all possible geometrically constrained topologies through an evaluation of the residue contact energy formed by the secondary structures, instead of the entire chain. We developed a contact pair specific and distance specific multiwell function based on the statistical characterization of the side chain distances of 413 proteins in the Protein Data Bank. The multiwell function has specific parameters to each of the 210 pairs of residue contacts. We illustrated a general mathematical method to extend a single well function to a multiwell function to represent the statistical data. We have performed a mutation analysis using 50 proteins to generate all the possible geometrically constrained topologies of the secondary structures. The result shows that the native topology is within the top 25% of the list ranked by the effective contact energies of the secondary structures for all the 50 proteins, and is within the top 5% for 34 proteins. As an application, the method was used to derive the structure of the skeletons from a low resolution density map that can be obtained through electron cryomicroscopy. Proteins 2009. © 2009 Wiley‐Liss, Inc.     

DNA and RNA oligomer thermodynamics: The effect of mismatched bases on double-helix stability

The thermodynamic parameters for the double-strand formation of the molecules rCAmG + rCU_nG, m,n = 5–7, and dCA_mG + dCT_nG, m,n = 5,6, were measured from optical melting curves. Normal helices are formed when m = n. The deoxyoligomers are more stable than the ribo-oligomers, due to a more favorable enthalpy. Double helices with mismatched bases can be formed by mixing oligomers with m ≠ n. Such helices may form several possible structures. A structure with a dangling base is favored over a structure with a bulged base. The destabilization of the double strands by the formation of a bulged base was determined to be greater than 1.6 kcal/mol at 10°C. The extent of aggregation in the oligomer double strand rCA₇G·rCU₇G was determined using ultracentrifugation equilibrium. The possible effects of aggregation on the determination of the thermodynamic parameters for double-strand formation are discussed.